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How Protein Crystallography Revolutionizes Drug Design

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A 21st century goal: Making rational drug design as simple as LEGOs.

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A 21st century goal: Making rational drug design as simple as LEGOs.

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D.1.1 List the effects of medicines and drugs on the functioning of the body.

Drug or medicine is a substance that does one or more of the following:

The active ingredients in drugs and medicines can be isolated from a plants and animals or synthesized artificially.

Drugs supposed to assist human body's natural self-healing capabilities.

Placebos are drugs containing no active ingredient, which "fool" the human body into healing.

D.1.2 Outline the stages involved in the research, development and testing of new pharmaceutical products.

The research and development of new medicines is a long and costly process. It usually takes up to 12 years and costs more than $200 million.

2. The drug is tested on animals. LD ₅₀ and ED ₅₀ are determined.

a. Human Pharmacology - testing on small group of healthy volunteers for safety

is a lethal dose necessary to kill 50 percent of animal population. is an effective dose, one creating a noticeable effect in 50% of animal population. The ratio between and is called the Therapeutic Index.

Therapeutic determines a safety of drug. If the therapeutic index of a drug is 10, a person would have to intake ten times more drug than the effective dose for the effects to be lethal. According to the therapeutic index, the researchers decide whether a dosage must be controlled. If TI is low, the dosage must be closely controlled.

During testing, half of the patients receive a real drug and the other half similar-looking placebo. This determined whether the drug has a real effect or the pill only fooled body into healing.

NOTE: We must know Thalidomide as an example of what can go wrong during R&D process of a drug. Thalidomide alleviates morning sickness during pregnancy. The drug's development revealed severe side effects - babies, whose mothers used the medicine, got born with deformed limbs.

D.1.3 Describe the different methods of administering drugs.

There are five ways of administering a drug:

D.1.4 Discuss the terms therapeutic window, tolerance and side-effects.

Therapeutic window - the difference between the effective dose and lethal dose; also called therapeutic index

Side effects - the undesired effects of drugs

Ex: aspirin thins the blood (used as an anti-clotting agent to prevent a hearth attack)

Morphium, the pain reliever, causes constipation.

Tolerance - a person taking a drug often gets used to the active ingredient, so it takes larger and larger doses to obtain the drug's desired effect. There is a danger that a body would create a physical addiction to a drug. For instance, an addiction to caffeine: if the addict does not get his/her coffee, he/she gets headaches. Another issue is that with increasing dose, the user is coming closer and closer to the lethal dose.

Risk-to-benefit ratio - determines whether the side effects (risk) of the drug are acceptable in relation to its curing effects; for example, a drug curing baneful disease would be accepted despite high risks

D.2.1 State and explain how excess acidity in the stomach can be reduced by the use of different bases.

Human stomach contains gastric juices secreted by some cells of the stomach walls. The gastric juices are acidic, with pH between 1.0 and 3.0, because they contain hydrochloric acid (HCl). Excessive acid production causes heartburn and damage of the mucus covering the walls of the stomach. Moreover, excess production of acid creates an ideal environment for the bacteria Helicobacter pylori, causing peptic ulcers.

Hearthburn - the situation when gastric juices overflow through esophagus

Ulcers - scars on the walls of stomach, indirectly caused by an excessive acidity.

Antacids are weak bases, utilized to neutralize the excess acidity in a human stomach. They relieve the pain of ulcers and prevent ulcers and heartburn from happening. Antacids are metal oxides, hydroxides, carbonates or hydrogencarbonates.

Common ingredients of antacids are alginates and anti-foaming agents.

Alginates create a layer of mucus on the walls of stomach and in esophagus, which prevents the heartburn.

agents prevent flatulence (farting) and burping. A common anti-foaming agent is Anti-foaming dimethicone.

D3 Anelgesics

D.3.1 Describe and explain the different ways that analgesics prevent pain.

Analgesics are drugs that relieve pain. They can be mild or strong.

Mild analgesics intercept the pain stimulus at its source. Modes of operation: (1) interfere with the production if prostaglandins, chemicals that cause pain; (2) reduce fever; (3) reduce swelling.

Strong analgesics (narcotics) relieve pain by temporarily bonding to the pain receptors in in the brain. They prevent the transmission of pain impulses into the brain.

D.3.2 Describe the use of derivatives of salicylic acid as mild analgesics and compare the advantages and disadvantages of using aspirin and paracetamol (acetaminophen).

Salicylic acid was an analgesic obtained from the bark of willow trees. However, salicylic acid had severe side effects. Therefore, researchers modified the structure of salicylic acid, creating derivatives. Derivative molecules mean they have different active groups attached to them.

Derivatives of salicylic are used as mild analgesics. They control the release of prostaglandins and thus reduce pain. Two examples of derivatives of salicylic acid are aspirin and paracetamol. Both medicines are painkillers and reduce fever (antipyretic). However, only aspirin reduces inflammation.

D.3.3 Compare the structures of morphine, codeine and diamorphine (heroin, a semi-synthetic opiate).

Morphine, codeine and diamorphine (heroin) are powerful strong analgesics, which block the perception of pain in the brain.

Morphine and codeine are obtained from the opium (found in the puppy plants). Low concentrations of heroin can be found in opium; however, this drug is usually prepared synthetically.

Morphine + ethanoic acid → heroin + water

The reaction between morphine and ethanoic acid is a condensation reaction. The acid reacts with alcohol groups in morphine (also referred to as hydroxy or -OH groups). The product of the reaction is water and heroin.

D.3.4 Discuss the advantages and disadvantages of using morphine and its derivatives as strong analgesics.

D4 Depressants

Tranquilizers (alcohol, valium) reduce nervous tension without inducing sleep in moderate doses.

D.6 Antibacterials

D.7 Antivirals

D.7.1 State how viruses differ from bacteria.

1) viruses are 20x smaller than bacteria;

2) unlike bacteria viruses are not cellular - bacteria have cell wall and nucleus

3) viruses do not have cytoplasm, while bacteria do

4) viruses do not feed, excrete and grow, while bacteria does

5) viruses use cell material of the invaded cell to reproduce themselves, while bacteria use cell division

Viruses inject their RNA or DNA into their host cell's cytoplasm and use the cell to replicate. The new cell either releases the virus or releases other infected cell. This change in cell structure cause symptoms of viral infection.

D.7.2 Describe the different ways in which antiviral drugs work.

1) Prevent viruses from leaving the host cell.

2) Block the reverse transcriptase enzyme activity to avoid a conversion of the virus into a form that can enter the host cell.

3) Alter the host cell's genetic material, so that viruses cannot use it to multiply.

4) Block the enzyme activity within the host cell, so viruses cannot multiply.

D.7.3 Discuss the difficulties associated with solving the AIDS problem

The antiviral agents are very expensive, which makes treatment of HIV difficult in developing countries. People cannot afford the drugs.

There are sociocultural issues fostering the spread of HIV, too:

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D.1.1 List the effects of medicines and drugs on the functioning of the body. Drug or medicine is a substance that does one or more of the following: The active ingredients in drugs and medicines can be isolated from a plants and animals or synthesized artificially.

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What factors affect your choice of a drug you take when in pain or feeling sick?

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What factors affect your choice of a drug you take when in pain or feeling sick?

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Do you have any positive/ negative experiences of taking drugs? 

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Do you have any positive/ negative experiences of taking drugs? 

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what do you do when you have a headache? How would you choose a drug for headache or skin allergy? 

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what do you do when you have a headache? How would you choose a drug for headache or skin allergy? 

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What are the different ways drugs can be administered? Which is the best way? 

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What are the different ways drugs can be administered? Which is the best way? 

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What are some common analgesics? Have you taken any recently? How do you think these analgesics affect you in the long run?

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What are some common analgesics? Have you taken any recently? How do you think these analgesics affect you in the long run?

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refer to this pdf file from your textbook to refer and make notes

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Watch this youtube video as an introduction to Medicinal chemistry

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Watch this youtube video as an introduction to Medicinal chemistry

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This page will lead you to topic1- D1. Here are some resources you can look up.

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Medicinal Chemistry.pptx - Microsoft PowerPoint Online